NM_001366737.1:c.-1-2205G>A

Variant names:

• chr5-75032243-C-T
• rs7734427
• NM_001366737.1:c.-1-2205G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366737.1(GCNT4):​c.-1-2205G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,982 control chromosomes in the GnomAD database, including 14,277 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (14277 hom., cov: 31)
• Consequence: GCNT4 NM_001366737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 4 publications found

Genes affected

GCNT4 (HGNC:17973): (glucosaminyl (N-acetyl) transferase 4) Predicted to enable acetylglucosaminyltransferase activity. Predicted to be involved in O-glycan processing and carbohydrate metabolic process. Predicted to act upstream of or within several processes, including inter-male aggressive behavior; kidney morphogenesis; and thyroid hormone metabolic process. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCNT4	NM_001366737.1	c.-1-2205G>A		intron_variant	Intron 3 of 3	ENST00000652361.2	NP_001353666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCNT4	ENST00000652361.2	c.-1-2205G>A		intron_variant	Intron 3 of 3		NM_001366737.1	ENSP00000498836.1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59810 AN: 151864 Hom.: 14253 Cov.: 31

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.390

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.394 AC: 59904 AN: 151982 Hom.: 14277 Cov.: 31 AF XY: 0.390 AC XY: 28968 AN XY: 74286

African (AFR) AF: 0.682 AC: 28223 AN: 41398

American (AMR) AF: 0.341 AC: 5205 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3470

East Asian (EAS) AF: 0.256 AC: 1323 AN: 5164

South Asian (SAS) AF: 0.328 AC: 1580 AN: 4814

European-Finnish (FIN) AF: 0.275 AC: 2906 AN: 10584

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18357 AN: 67966

Other (OTH) AF: 0.388 AC: 817 AN: 2108

Alfa AF: 0.308 Hom.: 4306

Bravo AF: 0.417

Asia WGS AF: 0.311 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.20
PhyloP100		0.053

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7734427; hg19: chr5-74328068; COSMIC: COSV107374541;